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improve update.py #1536

Merged
merged 107 commits into from
Jul 21, 2022
Merged

improve update.py #1536

merged 107 commits into from
Jul 21, 2022

Commits on Apr 28, 2022

  1. remove unused import

    @fabianegli
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  2. use early return pattern

    @fabianegli
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  3. bug fix: variable name

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  4. use f string instead of format

    @fabianegli
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  5. do not use f-strings unnecessarily

    @fabianegli
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Commits on Apr 29, 2022

  1. use nested unpacking

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  2. wrapping f-strings

    @fabianegli
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  3. say updates complete only after updates

    @fabianegli
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  4. use a list comprehension

    @fabianegli
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  5. fail if the arguments are incompatible

    @fabianegli
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  6. adopt isort

    @fabianegli
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  7. remove unused import

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  8. use import from

    @fabianegli
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  9. use list comprehension

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  10. let tempfile chose a temporary directory

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  11. collect parameter test prompt+sha

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  12. collect parameter test module+all

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  13. raise UserWarning instead of return

    @fabianegli
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  14. remove unused import

    @fabianegli
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Commits on May 5, 2022

  1. click doesn't handle mutually exclusive flags

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Commits on May 12, 2022

  1. Fix nf-core#1419

    @drpatelh @fabianegli
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  2. Black

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  3. Handle missing key, log, call after web builder

    @ewels @fabianegli
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  4. Deep copy of schema not needed

    @ewels @fabianegli
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  5. Format strings

    @ewels @fabianegli
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  6. print include statement when installing a module

    @fabianegli
    Júlia Mir Pedrol authored and fabianegli committed May 12, 2022
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  7. resolved rebase merge conflict

    @fabianegli
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  8. remove remove stringtie special case

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  9. Update actions_ci.py 

    In cases where e.g. multiple aligners are specified in the GitHub Actions matrix, trying to pull a 'NXF_VER' key out of the include dictionary can cause line 140 to fail when it shouldn't. The get() method will not error if the key is not present, fixing this problem.
    @njspix @fabianegli
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  10. resolve rebase mergeconflicts

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  11. run tests with pytest

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  12. remove test workflow check

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  13. add code tests

    @fabianegli
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  14. fix linting

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  15. apply comments from PR review

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  16. fix linting

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  17. apply comments from PR

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  18. fix test

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  19. always set profile

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  20. do not abbreviate env var

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  21. add new test

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  22. update CHANGELOG

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  23. specify test files as test_*.py in pytest.ini

    @fabianegli
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  24. apply comments from PR review

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  25. check if profile is available

    @fabianegli
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  26. modify linting

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  27. Add nf-core/modules folder warning 

    Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
    @mirpedrol @ggabernet @fabianegli
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  28. Add valid profile check 

    Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
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  29. fix linting

    @mirpedrol @fabianegli
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  30. avoid using shell=True when checking profile

    @mirpedrol @fabianegli
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  31. Apply suggestions from code review 

    Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
    @mirpedrol @ewels @fabianegli
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  32. remove unnecessary libraryes

    @mirpedrol @fabianegli
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  33. replace a weird with a normal dash

    @fabianegli
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  34. add documentation for modules mulled command

    @mirpedrol @fabianegli
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  35. add documentation for modules test command

    @mirpedrol @fabianegli
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  36. Add biocontainers reference 

    Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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  37. First stab at writing a central utils function for GitHub API calls. 

    Uses authentication from local gh CLI or a supplied bearer token if found.

Done to address nf-core#1496

Bit scared it'll break something, so ideally needs extensive testing.
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  38. Remove superfluous dict() call

    @ewels @fabianegli
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  39. Fix sync pytests

    @ewels @fabianegli
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  40. Better debug logging. 

    Also removed function prefix from calls that were in the same file
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  41. Try to rewrite GitHub API calls to use a single shared Session

    @ewels @fabianegli
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  42. Use new class more in the sync code

    @ewels @fabianegli
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  43. Nearly fix the tests

    @ewels @fabianegli
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  44. Better exception handling / logging for gh auth failure

    @ewels @fabianegli
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  45. Use XDG_CONFIG_HOME or ~/.config/nf-core/ for the requests cache dir. 

    Suggested by @emiller88 👍🏻
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  46. resolve merge conflicts after rebase Changelog

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  47. Apply suggestions from code review 

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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  48. Update nf_core/sync.py 

    Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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  49. Merge branch 'dev' into fabianegli-update-refactor

    @fabianegli
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  50. Fix wrong merge conflict resolution

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  51. if-else instead of if-if

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  52. collect more parameter checks

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Commits on May 25, 2022

  1. Merge branch 'nf-core:master' into fabianegli-update-refactor

    @fabianegli
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  2. Merge branch 'dev' into fabianegli-update-refactor

    @fabianegli
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  3. Merge branch 'fabianegli-update-refactor' of github.com:fabianegli/to… 

    …ols into fabianegli-update-refactor
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  4. Merge branch 'dev' into fabianegli-update-refactor

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Commits on May 27, 2022

  1. Merge branch 'dev' into fabianegli-update-refactor

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Commits on Jun 1, 2022

  1. Merge branch 'dev' into fabianegli-update-refactor

    @fabianegli
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  2. Merge branch 'dev' into fabianegli-update-refactor

    @fabianegli
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  3. Merge branch 'fabianegli-update-refactor' of github.com:fabianegli/to… 

    …ols into fabianegli-update-refactor
    @fabianegli
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  4. fix missing import after merge conflict resolution

    @fabianegli
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Commits on Jul 20, 2022

  1. Merge branch 'dev' of github.com:nf-core/tools into fabianegli-update… 

    …-refactor
    @ErikDanielsson
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  2. Fix failing test due to merge

    @ErikDanielsson
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  3. Move --all or not code to methods

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  4. Move more stuff to methods

    @ErikDanielsson
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  5. Refactor dry run stuff into methods

    @ErikDanielsson
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  6. Always move files to temp dir first, to make sure the installation wo… 

    …rks before removing files
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  7. Move mod json diff to method

    @ErikDanielsson
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  8. Move the update method

    @ErikDanielsson
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  9. fix variable name

    @fabianegli
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  10. More misc. refactoring

    @ErikDanielsson
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  11. Merge branch 'fabianegli-update-refactor' of github.com:fabianegli/to… 

    …ols into fabianegli-update-refactor
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  12. Fix tests

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  13. Don't pass install folder as a list

    @ErikDanielsson
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  14. Fix install dir issue in ModulesJson

    @ErikDanielsson
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  15. Update CHANGELOG.md

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Commits on Jul 21, 2022

  1. Update CHANGELOG.md 

    Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
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  2. Fix short flag of '--show-diff' and update CHANGELOG

    @ErikDanielsson
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  3. some docstring improvements

    @fabianegli
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  4. use questionary.path for file name input

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  5. break too long line

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  6. ensure diff file exists after diff file setup

    @fabianegli
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  7. Fix changelog

    @ErikDanielsson
    ErikDanielsson committed Jul 21, 2022
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  8. Merge branch 'fabianegli-update-refactor' of github.com:fabianegli/to… 

    …ols into fabianegli-update-refactor
    @ErikDanielsson
    ErikDanielsson committed Jul 21, 2022
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  9. Merge branch 'dev' of github.com:nf-core/tools into fabianegli-update… 

    …-refactor
    @ErikDanielsson
    ErikDanielsson committed Jul 21, 2022
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  10. Update docs

    @ErikDanielsson
    ErikDanielsson committed Jul 21, 2022
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  11. Merge branch 'dev' of github.com:nf-core/tools into fabianegli-update… 

    …-refactor
    @ErikDanielsson
    ErikDanielsson committed Jul 21, 2022
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